Contacts of the helix formed by residues 104 - 115 (chain D) in PDB entry 1XBT
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 104 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80D LEU* 3.8 15.0 - - + +
81D LEU* 3.1 25.2 + - - +
82D ARG* 3.0 36.6 + - - +
102D PHE* 3.7 9.5 - - - +
103D PRO* 1.3 80.7 - - + +
105D ILE* 1.3 62.3 + - - +
106D VAL 3.3 3.3 + - - -
107D GLU* 3.3 14.9 + - + +
108D PHE* 3.1 24.7 + - + +
107G GLU* 3.6 25.5 - - + +
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Residues in contact with ILE 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81D LEU* 3.7 20.0 - - + -
96D ILE* 4.1 6.7 - - + -
99D GLY* 3.8 34.1 - - - +
100D GLN* 5.9 0.7 - - - +
102D PHE* 3.3 20.0 + - + +
103D PRO 3.4 0.8 - - - +
104D ASP* 1.3 78.1 + - - +
106D VAL* 1.3 75.6 + - + +
108D PHE* 3.9 0.5 - - - +
109D CYS* 3.1 47.1 + - - -
121D VAL* 4.0 11.4 - - + -
135D ALA* 4.4 22.2 - - + +
136D ILE* 4.6 7.4 - - + +
139D LEU* 4.0 17.5 - - + -
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Residues in contact with VAL 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104D ASP 3.3 1.0 - - - -
105D ILE* 1.3 83.2 - - + +
107D GLU* 1.3 68.6 + - - +
109D CYS* 4.0 1.0 - - - +
110D GLU* 3.0 32.2 + - - +
135D ALA* 3.9 14.8 - - + +
138D ASN* 3.5 37.7 - - + +
139D LEU* 4.0 12.9 - - + +
142D LEU* 3.7 16.8 - - + -
82G ARG* 3.3 33.2 - - - +
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Residues in contact with GLU 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D PRO 3.7 6.9 - - - +
104D ASP* 3.3 26.7 - - + +
106D VAL* 1.3 86.4 + - - +
108D PHE* 1.3 58.4 + - - +
110D GLU* 4.1 0.5 - - - +
111D ALA* 3.0 31.7 + - - +
80G LEU* 5.5 1.9 - - - +
82G ARG* 4.4 20.8 + - + +
104G ASP* 3.3 25.9 - - + +
107G GLU* 3.3 38.8 - - + -
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Residues in contact with PHE 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D ILE* 4.3 12.1 - - + -
81D LEU* 3.6 53.4 - - + -
82D ARG* 4.6 1.3 - - - -
84D VAL* 5.1 0.2 - - + -
85D ALA* 4.2 7.0 - - + -
88D ALA* 3.8 24.5 - - + -
94D ILE* 4.3 8.5 - - + -
96D ILE* 3.7 25.4 - - + -
104D ASP* 3.1 22.4 + - + +
107D GLU* 1.3 75.3 - - - +
109D CYS* 1.3 63.0 + - - +
111D ALA* 3.3 3.8 + - - +
112D MET* 2.9 68.9 + - + +
119D VAL* 5.0 1.6 - - + -
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Residues in contact with CYS 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D ILE* 3.6 22.0 - - + +
96D ILE* 3.9 7.0 - - - -
105D ILE* 3.1 37.9 + - - +
108D PHE* 1.3 79.7 - - - +
110D GLU* 1.3 59.3 + - - +
112D MET* 3.4 1.2 + - - +
113D ALA* 2.9 32.2 + - - +
119D VAL* 3.7 17.9 - - + +
121D VAL* 3.7 29.6 - - - -
139D LEU* 3.8 11.4 - - + -
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Residues in contact with GLU 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B ARG* 2.2 39.4 + - - -
186B ARG* 3.0 22.8 + - - -
190B PHE* 3.6 2.3 - - - -
21D ILE* 3.8 5.2 - - - +
106D VAL 3.0 18.9 + - - +
107D GLU 4.1 2.5 - - - +
109D CYS* 1.3 77.3 - - - +
111D ALA* 1.3 55.7 + - - +
113D ALA* 3.9 0.7 - - - +
114D ASN* 3.0 54.9 + - - +
142D LEU* 3.7 21.1 - - + +
82G ARG* 4.1 29.4 - - + +
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Residues in contact with ALA 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D GLU 3.0 20.2 + - - +
108D PHE* 3.8 4.3 - - - +
110D GLU* 1.3 77.0 - - - +
112D MET* 1.3 62.9 + - + +
114D ASN* 3.5 6.6 + - - +
115D ALA* 3.1 28.6 + - - +
111G ALA* 6.2 3.6 - - + -
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Residues in contact with MET 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85D ALA* 4.0 19.5 - - + +
88D ALA* 4.1 6.1 - - + +
89D LEU* 3.7 33.7 - - + -
94D ILE* 3.8 26.2 - - + -
108D PHE* 2.9 53.0 + - + +
111D ALA* 1.3 79.1 - - + +
113D ALA* 1.3 62.9 + - - +
115D ALA* 3.2 10.3 + - - +
116D GLY 3.3 0.2 + - - -
117D LYS* 3.0 32.9 + - + +
119D VAL* 3.7 19.7 - - + -
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Residues in contact with ALA 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186B ARG* 3.6 32.1 - - - +
19D GLY* 3.2 17.3 + - - -
20D GLN 3.8 13.2 - - - +
21D ILE* 3.7 14.6 - - + -
109D CYS 2.9 19.2 + - - +
110D GLU 3.9 0.2 - - - +
112D MET* 1.3 75.8 - - - +
114D ASN* 1.3 58.8 + - - +
116D GLY* 3.1 13.5 + - - -
117D LYS 3.5 10.8 - - - -
119D VAL* 4.2 1.0 - - + +
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Residues in contact with ASN 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186B ARG* 3.0 30.8 + - - +
187B LEU* 6.0 1.6 - - - +
190B PHE* 3.7 22.7 - - - -
110D GLU* 3.0 43.6 + - - +
111D ALA* 3.9 6.6 - - - +
113D ALA* 1.3 73.8 - - - +
115D ALA* 1.3 57.0 + - - +
116D GLY 3.2 3.4 + - - -
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Residues in contact with ALA 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89D LEU* 5.3 8.5 - - + -
111D ALA 3.1 17.3 + - - +
112D MET* 3.2 6.9 + - - +
114D ASN* 1.3 74.3 - - - +
116D GLY* 1.3 58.6 + - - +
117D LYS* 3.5 21.3 + - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il